Cancer Epigenetics. Epigenetics refers to a switch between phenotypic states that is not based upon a change in genotype, such as a mutation, but is the result of a change in gene activity without any accompanying alteration of the DNA sequence. Simply put, this amounts to a stable change in gene expression. In cancer epigenetics, the most commonly observed situation is a change from a transcriptionally active gene to an epigenetically ‘silenced’ state. Epigenetic alterations are distinct from transitory changes in gene regulation, in that they involve relatively extensive, stable changes in chromatin structure, histone modification, associated protein composition, and in many cases, altered distribution of cytosine-5 DNA methylation at CpG dinucleotides in, for example, the promoter region of the gene. Of all of these molecular mechanisms, DNA methylation is the easiest to measure in archival samples, because cytosine methylation is retained in the genomic DNA throughout, for example, formalin-fixation, years of storage in paraffin blocks, and subsequent extraction from paraffin sections. Even heavily degraded, crosslinked DNA can be subjected successfully to DNA methylation analysis using, for example, bisulfite-based technique (e.g., with PCR amplicons, as is the case for the MethyLight™ technology).
The main targets for epigenetic gene silencing in cancer cells are promoter regions containing G:C- and CpG-rich stretches of DNA, called ‘CpG islands.’CpG islands are G:C and CpG-rich stretches of DNA in the genome, often located in the vicinity of genes, and generally unmethylated in normal somatic tissues. Aberrant methylation of CpG islands has, for example, been documented in both benign and malignant human colorectal tumors and is associated with gene silencing.
It is important to note, however, that not all epigenetically silenced genes in cancer cells are tumor-suppressor genes, and that many of the affected CpG islands are not even located in promoter regions, and are not thought to affect gene expression (e.g., they may be in promoter regions of genes that are not expressed in either the normal or malignant cells of an organ giving rise to a malignancy). Yet, the occurrence of CpG island hypermethylation events is, in many cases, cancer-specific, suggesting a scenario in which the overall rate of CpG island hypermethylation during tumorigenesis needs to be sufficiently high to acquire the necessary hits at key loci, but at the same time perhaps affecting many other loci which are essentially innocent bystanders.
CIMP in colorectal cancer; prior art uncertainty and inconsistencies. A subset of colorectal tumors has been described to have an unusually high number of hypermethylated CpG islands, leading to the definition of a distinct phenotype, referred to as “CpG Island Methylator Phenotype”, or “CIMP” (16, 21). Colorectal cancer has a lifetime incidence of 1 in 20, and CIMP cancers account for at least 15% of this, representing a large cohort of affected patients. Colorectal cancer has been traditionally been considered to be a single disease for the purposes of treatment, but recent evidence has suggested that there are different outcomes in sub-groups with distinct molecular features. Such CIMP+ colorectal tumors have been reported to have distinct profiles of genetic alterations, anatomic subsite, gender prevalence, histopathologic characteristics and clinical behavior.
However, a clear understanding of the CIMP phenomenon has been hampered by two complexities. First, the intricacy of the relationship between CIMP and microsatellite instability continues to result in different perspectives on the issue (38, 77). Second, the concept that CIMP affects only a subset of colorectal tumors and a subset of CpG islands, as opposed to all CpG islands known to be susceptible to hypermethylation, is not universally embraced or appreciated (38), and is further complicated by the fact that there are no firm rules for recognizing which CpG islands belong to the CIMP group. An initial panel of cancer-specifically methylated CpG island markers (21) has not been applied consistently in the literature, nor does it appear that all cancer-specifically methylated genes are affected by CIMP. Nevertheless, it seems clear that some CpG islands are more prone to cancer-specific hypermethylation than others. Thus, a lack of standardization in the classification methods used to define CIMP has resulted in varying and contradictory conclusions regarding, or example, the association of CIMP with a family history of cancer, and even the very existence of CIMP as a distinct subgroup of colorectal tumors. Not only has there been some ambiguity as to which CpG islands belong to the CIMP subset, but there has also been a lack of a uniform standard for applying this subset to the definition of CIMP status. The existence of unique CIMP-related etiologic and pathogenetic mechanisms can only be defined when this subgroup can be clearly and accurately identified. There are presently no clear guidelines for what constitutes CIMP-associated versus non-CIMP-associated CpG islands.
Therefore, there is a pronounced need in the art to further elucidate and understand the epidemiology and etiology of DNA methylation alterations in human colorectal cancer, and to clarify the uncertainties regarding the existence of CIMP and its classification. There is a pronounced need in the art to not only unambiguously confirm the existence of CIMP as a distinct subgroup of colorectal cancer, but also to establish an improved CIMP classification panel of methylation markers. There is a pronounced need in the art to provide compositions and methods for determining the relationship between CIMP status and molecular, demographic, and histopathologic features, and environmental risk factors. There is a pronounced in the art to understand the pathogenesis of this colorectal cancer subset and its association with risk factors so that we will be better placed to prevent its occurrence. There is a pronounced in the art to correctly identify cases which will best respond to particular therapies.